Sample patient with all FHIR resources

[Chandan Datta]

Hi all,

I have setup the smart-installer. Is there any patient with all the FHIR data such as allergies, immunizations, Family History, Documents etc?

[Nikolai Schwertner]

Allen Vitalis features a variety of resources

On 12/13/14 7:15 PM, Chandan Datta wrote:

Hi all,

I have setup the smart-installer. Is there any patient with all the FHIR data such as allergies, immunizations, Family History, Documents etc?

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[Chandan Datta]

After installing the FHIR server, I searched for Allen, but can't see. Only these:

♂ Daniel X. Adams Dec 23, 1925

♂ Brian Q. Gracia Jun 22, 1965

♂ Stephan P. Graham May 1, 1945

♂ Robert P. Hill Oct 27, 1953

♀ Carol U. Hughes Nov 4, 1949

♂ Daniel A. Johnson Feb 22, 1995

♂ Joseph I. Ross Oct 2, 2003

♀ Amy V. Shaw Mar 20, 2007

♂ Patrick G. Taylor Oct 15, 2004

♂ Joshua P. Williams Aug 21, 1954

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Regards,
Chandan

[Josh Mandel]

Hi Chandan,

By default the automatic build includes only 10 patients. You can update your custom settings to increase the 
sample_patients_limit" to include our full set of ~60 patients via:

sample_patients_limit: 1000

(Note: we added this limit just so people could quickly stand up a server and try things out -- but this may be "surprising" behavior. I've added a note to the README, at least. We should also consider updating the default limit to include all patients.)

[Chandan Datta]

Hi Josh,

Thank for that.

I added the sample_patient_limit to the file custom_settings.yml as well as increased in provisioning/roles/common/defaults/main.yml to 1000  , but none of the changes worked after doing an ansible rebuild. Is there any test code to query the database sever to check whether the build is getting through.

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Regards,
Chandan

[Nikolai Schwertner]

Hmm. Perhaps try to set ' force_rebuild' to 'true':
https://github.com/smart-on-fhir/installer/blob/master/provisioning/roles/common/defaults/main.yml#L20

[Chandan Datta]

Hi Nikolai,

The last build went through fine and it is working now

[Chandan Datta]

Is there a way to add Family history, Dispenses, allergies to Allen (id 99912345) ?

{

  "resourceType": "Bundle",

  "title": "FHIR Atom Feed",

  "id": "http://128.199.XXX.XXX:9080/FamilyHistory/_search?subject%3APatient=99912345",

  "link": [

    {

      "rel": "self",

      "href": "http://128.199.XXX.XXX:9080/FamilyHistory/_search?subject%3APatient=99912345"

    }

  ],

  "totalResults": 0,

  "updated": "2014-12-19T20:38:25.503-05:00",

  "author": [

    {

      "name": "groovy.config.atom.author-name",

      "uri": "groovy.config.atom.author-uri"

    }

  ]

}

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Regards,
Chandan

[Nikolai Schwertner]

You can, by editing the data files in:
https://github.com/smart-on-fhir/sample-patients/tree/master/data

[Jean-Michel Lavarenne]

Hi,

How would I go about creating practitioner sample data?

To be more precise, I want to include practitioner sample data and also create a relationship reference to immunization resources, to make this available as Immunization.performer.

Can that change be accommodated by the existing immunization.txt csv file?

Thanks!

[Nikolai Schwertner]

Hi Jean-Michel,

Unfortunately, we don't have a generic mechanism for creating practitioner sample data. In our sample patient set, we only provide one sample practitioner. The practitioner is generated with this template:
https://github.com/smart-on-fhir/sample-patients/blob/master/bin/fhir_templates/practitioner.xml

As for the immunizations, our sample patient generator does not include performer data (see https://github.com/smart-on-fhir/sample-patients/blob/master/bin/fhir_templates/immunization.xml) and the underlying data source file does not have a provision for it. However, you are welcome to extend the generator however you see fit.

Best,
Nikolai

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[Jean-Michel Lavarenne]

Hi Nikolai,

Thanks for your answer, it looks like what I need to do.

In a nutshell, is it correct that what I need to do is update the generate.py file to write FHIR xml to the /generated_data directory and then I can expect the data to be available in my local install of the SMART sandbox after provisioning?

Best regards,

JM 

[Nikolai Schwertner]

This is correct, for the most part, assuming that you properly configure the installer to use your sample patients builder instead of the public one that we are hosting. Alternatively, you can use the generator to build your patient data files in FHIR format outside the context of the installer and then push them to your API server from the command line (see how we are doing it in the build script https://github.com/smart-on-fhir/installer/blob/master/provisioning/roles/common/tasks/sample-data.yml#L48)/

Most likely, you won't have to change anything in "generate.py", but instead in "fhir.py", "immunizations.py", the immunizations template and data file.

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[Jean-Michel Lavarenne]

Thanks for that pointer, Nikolai.  Can I expect it to work with json too?  I am trying the following with no success:

curl -u client:secret 'http://localhost:3000/?' -H 'Content-Type: application/json' --data-binary @my-app.json

I get an xml error message back:

<OperationOutcome xmlns="http://hl7.org/fhir">

  <issue>

    <severity value="error"/>

  </issue>

</OperationOutcome>

[Josh Mandel]

Should work in JSON and XML -- but you'll want to set an "Accept" header to indicate the format of response you want back. (Given the error you're seeing, I'm guessing you'll just get a JSON-encoded version of the same unhelpful OperationOutcome.)

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[Jean-Michel Lavarenne]

Thanks Josh, I got it to work with the sample json in the custom-data directory.  I must be having formatting issues with the json I am attempting to import, or else missing requirements and expectations about elements that I don't know about yet.

[Paul Laoha]

Hi,

I'm trying to add more immunization data but am receiving this error:

{

  "resourceType": "OperationOutcome",

  "issue": [

    {

      "severity": "error",

      "details": {

        "text": "Cannot cast object 'value=\"1\"' with class 'org.apache.xerces.dom.DeferredAttrNSImpl' to class 'float'"

      }

    }

  ]

}

The data I'm trying to add looks as follows:

"vaccinationProtocol": [

   {

    "doseSequence": "1",

    "series": "Havrix",

    "seriesDoses": "2"

  }

]

I believe the doseSequence is not allowing me to pass in a positiveInt even though it is part of the FHIR standard.

Any suggestions on how to add this?

[Josh Mandel]

Thanks for the report, Paul. This is a bug in our server, specifically in the search indexing process, which we intend to fix. It is in our issues list (https://github.com/smart-on-fhir/api-server/issues/27)

Best,

Josh

[Paul L]

Hi,

I would like to ask another question related to patient data.  

Is there a recommended way to get immunization data from SMART on FHIR for vaccinations which have not occured yet?  For instance, suppose I'm looking at HepB and it requires 3 vaccinations but the patient has only done 1 based on immunization history.  Would there be a standard way to get the information for the other 2 incomplete vaccination events still to occur.

http://www.cdc.gov/vaccines/schedules/easy-to-read/child-easyread.html

Regards,

Paul

On Saturday, December 13, 2014 at 4:15:15 PM UTC-8, Chandan Datta wrote:

[Josh Mandel]

Hi Paul,

The Immunization resource doesn't capture future plans, but you can use an ImmunizationRecommendation to capture specifically scheduled recommendations.

Best,

  Josh

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